Example Pipeline - Pathway Aggregation Analysis
Output
Data-Cleanup
Missingness
Missigness before removing buffer
plots_missingness
Log text:
missingness plots, missing values: 14853 out of 113400 (13.10%)
Missingness after removing buffer
plots_missingness
Log text:
missingness plots, missing values: 10227 out of 90720 (11.27%)
pre_filter_missingness
Log text:
features filtered, 50.00%, 39 of 630 removed
Missingness after filtering metabolites with more than 50% missing values per group
plots_missingness
Log text:
missingness plots, missing values: 6331 out of 85104 (7.44%)
plots_sample_boxplot
Log text:
sample boxplot, aes: color=Buffer
plots_sample_boxplot
Log text:
sample boxplot, aes: color=tissue
pre_norm_quot
Log text:
quotient normalization based on 36 reference samples and 511 variables: ~
Log text:
quotient normalization based on 36 reference samples and 511 variables: Buffer == “80% Meth + 20% H2O”
plots_dilution_factor
Log text:
dilution factor plot, ‘Buffer’
plots_sample_boxplot
Log text:
sample boxplot, aes: color=Buffer
pre_trans_log
Log text:
log2.000000
plots_sample_boxplot
Log text:
sample boxplot, aes: color=Buffer
pre_outlier_detection_univariate
Log text:
flagged 0 univariate outliers
reporting_data
Log text:
Dataset info: 144 samples, 591 features; 25 sample annotation fields, 10 feature annotation fields
write_se_xls
Log text:
Data exported to Excel file ‘PreprocessedData.xlsx’
Global Statistics
plots_umap
Log text:
UMAP, label_col: , aes: color=Buffer, size=2.5
plots_heatmap
Log text:
Heatmap of assay data.
plots_umap
Log text:
UMAP, label_col: , aes: color=tissue, size=2.5
plots_heatmap
Log text:
Heatmap of assay data.
plots_pca
Log text:
PCA, scores, label_col: , aes: color=Buffer, shape=tissue, size=2.5
modify_agg_pathways
Log text:
pathway aggregation by ‘Class’, 22 pathway scores generated
Pathway Aggregation Analysis
Buffer analysis
stats_univ_lm
Log text:
univariate lm, ~Buffer
post_multtest
Log text:
Multiple testing correction of ‘Buffer pw’ using ‘BH’
reporting_stats
Log text:
‘Buffer pw’ info
Samples: 50% Meth + 50% H2O: 36, 50% Meth + 50% PBS: 36, 80% Meth + 20% H2O: 36, 80% Meth + 20% PBS: 36 /// features: p.adj < 0.05, 7 of 22
plots_pval_hist
Log text:
P-value histograms for Buffer pw
plots_box_scatter
Log text:
Feature
Tissue analysis
stats_univ_lm
Log text:
univariate lm, ~tissue
post_multtest
Log text:
Multiple testing correction of ‘Tissue pw’ using ‘BH’
reporting_stats
Log text:
‘Tissue pw’ info
Samples: fat: 48, liver: 48, muscle: 48 /// features: p.adj < 0.05, 21 of 22
plots_pval_hist
Log text:
P-value histograms for Tissue pw
plots_box_scatter
Log text:
Feature
Multiple Statistics Heatmap
plots_multstats_heatmap
Log text:
Pheatmap of stat results. Colors represent (sign(statistic) * -log10(p.adj)))
Result Comparison
plots_stats_compare
Log text:
comparison plot between ‘Buffer pw’ and ‘Tissue pw’
